Well, yes, they do speculate in the abstract, note potentially there. It looks like authors do believe the variation is caused by manufacturing variation. But nothing in the paper actually shows it. There's no attempt to determine the cause of observed performance variation in the paper. An empirical survey.
Interestingly, that recommendation could be interpreted "empirical studies based on averaged node performance" give a very distorted view on "the true impact of manufacturing variation on processors".
The entire study seems to presuppose that most of what is measured is processor manufacturing variation. There's further recommendations about removing the variation with processor binning, etc.
It's an interesting set of measurements, but the assumed source of the variation is dubious, and it's not clearly what, if any, actions it really supports.
Interestingly, that recommendation could be interpreted "empirical studies based on averaged node performance" give a very distorted view on "the true impact of manufacturing variation on processors".